AMBER Archive (2008)

Subject: RE: AMBER: Amber9 with MPICH2 failure at runtime

From: Ross Walker (
Date: Wed Apr 16 2008 - 23:25:19 CDT

Hi Sasha,
The example you are using from the tutorial is a gas phase simulation and PMEMD doesn't support this. It should quit with an error message but sometimes running in parallel things don't quit cleanly.
The gas phase tutorial example is probably not a useful example for checking performance etc either since it really is an example of how "not to run" a simulation. I suggest trying the explicit solvent simulation in section 6.
This is much more typical of the types of calculations people would run.
All the best

|\oss Walker

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From: [] On Behalf Of Sasha Buzko
Sent: Wednesday, April 16, 2008 17:40
Subject: Re: AMBER: Amber9 with MPICH2 failure at runtime

Thank you for your reply, David.
make test.pmemd passed all tests. I also changed the number of processors to 8 and started another mpd on an additional node - I had 8 concurrent processes running. With that, it doesn't seem to be a problem with the pmemd executable.
I'll test it with a larger system, since apparently pmemd doesn't like the small 10-bp DNA fragment from an amber tutorial.



On Wed, 2008-04-16 at 17:26 -0700, David A. Case wrote:

On Wed, Apr 16, 2008, Sasha Buzko wrote:


> Speaking of pmemd, I did compile it and tried to run it on the same

> example from the tutorial. For some reason, I only get one pmemd process

> on one node and it just hangs there using up 100% of the cpu/core but

> not writing any output.

Did your pmemd pass the test suite? That would help narrow down the problem.

There doesn't need to be much pmemd documentation, since it should be a

drop-in replacement for sander (for the subset of sander tasks it can handle.)



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